It is well accepted that cancer is the result of the sequential mutations of oncogenes and tumor suppressor genes (1). Historically, the discovery of these genes has been accomplished through analyses of individual candidate genes chosen on the basis of functional or biologic data implicating them in the tumorigenic process. Recent advances in genomic technologies and bioinformatics have permitted simultaneous evaluation of many genes, thereby offering more comprehensive and unbiased information (2, 3). For example, the sequence of large families of genes, and even the human genes in the Reference Sequence (RefSeq) database, have been determined in subsets of human cancers (4, 5). However, the alterations detected by sequencing represent only one category of genetic change that occurs in human cancer. Other alterations include gains (amplifications) and losses (deletions) of discrete chromosomal sequences that occur during tumor progression. Dramatic amplifications of oncogenes such as ERBB2 (6) or MYC (7) and deletions of tumor suppressor genes such as CDKN2A (8), PTEN (9, 10) and SMAD4 (11) have demonstrated the importance of these mechanisms of genetic alteration in particular tumor types. A comprehensive picture of genetic alterations in human cancer should therefore include the integration of sequence based alterations together with copy number gains and losses.
Evaluations of copy number changes in cancers using a variety of array types have been previously reported (12). Several of the more recent studies employed oligonucleotide arrays capable of distinguishing >100,000 genomic loci in colon, breast lung, pancreatic, and skin cancers as well as certain leukemias (13-20). However, identification of focal, high copy amplifications or homozygous deletions (HDs) have infrequently been reported because many prior copy number analyses on arrays have used genomic DNA purified from primary tumors. Primary tumors contain varying proportions of non-neoplastic cells thereby reducing the apparent extent of amplification and obscuring focal amplifications—defined by the increased copy number of a small region of the genome—from simple gains of whole chromosome arms. Furthermore, HDs can be difficult to discern in primary tumors due to confounding hybridization signals from non-neoplastic cells (17).
Many of the problems encountered with primary tumor samples can be overcome by use of early passage cancer cell lines or xenografts which are devoid of human non-neoplastic cells. Previous studies have shown that the process of generating such in vitro or in vivo cultures is not associated with the development of additional genetic alterations (21). It is now widely recognized that HDs found in cell lines and xenografts represent true genetic alterations that are present in clonal fashion in primary tumors but are difficult to document in the latter because of contaminating non-neoplastic cells (22, 23).
There is a continuing need in the art for methods to characterize, classify, detect and diagnose breast and colorectal cancers.